bioconductor: mixOmics | Projects

10.3389/fonc.2020.00423

Computational Oncology in the Multi-Omics Era: State of the Art
Cited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: over 4 years ago

Untargeted In Silico Compound Classification—A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes
Cited by: 11
Author(s): Kristian Peters, Gerd Ulrich Balcke, Niklas Kleinenkuhnen, Hendrik Treutler, Steffen Neumann
Software Mentions: 31
Published: almost 4 years ago

10.1371/journal.pcbi.1005752

mixOmics: An R package for ‘omics feature selection and multiple data integration
Cited by: 1,902
Author(s): Florian Rohart, Benoît Gautier, Amrit Singh, Kim‐Anh Lê Cao
Software Mentions: 29
Published: about 7 years ago

10.1186/s40168-021-01100-2

Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation
Cited by: 31
Author(s): Anna Cäcilia Ingham, Katrine Kielsen, Hanne Mordhorst, Marianne Ifversen, Frank Møller Aarestrup, Klaus Müller, Sünje Johanna Pamp
Software Mentions: 18
Published: over 3 years ago

10.1186/s13059-020-02104-1

Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
Cited by: 57
Author(s): Matteo Calgaro, Chiara Romualdi, Levi Waldron, Davide Risso, Nicola Vitulo
Software Mentions: 17
Published: over 4 years ago

10.12688/f1000research.27268.1

rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis
Cited by: 16
Author(s): Sébastien Theil, Étienne Rifa
Software Mentions: 16
Published: almost 4 years ago

10.3389/fonc.2020.555632

Comprehensive Characterization of Alternative mRNA Splicing Events in Glioblastoma: Implications for Prognosis, Molecular Subtypes, and Immune Microenvironment Remodeling
Cited by: 8
Author(s): Liang Zhao, Jiayue Zhang, Zhiyuan Liu, Yu Wang, Shurui Xuan, Peng Zhao
Software Mentions: 16
Published: almost 4 years ago

10.3390/metabo9100222

Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species
Cited by: 29
Author(s): Kristian Peters, Hendrik Treutler, Stefanie Döll, Alida Kindt, Thomas Hankemeier, Steffen Neumann
Software Mentions: 15
Published: about 5 years ago

10.1038/s41598-021-81200-z

MuSA: a graphical user interface for multi-OMICs data integration in radiogenomic studies
Cited by: 11
Author(s): Mario Zanfardino, Rossana Castaldo, Katia Pane, Ornella Affinito, Marco Aiello, Marco Salvatore, Monica Franzese
Software Mentions: 15
Published: almost 4 years ago

10.3389/fchem.2021.734132

The “DOLPHINS” Project: A Low-Cost Real-Time Multivariate Process Control From Large Sensor Arrays Providing Sparse Binary Data
Cited by: 1
Author(s): Eugenio Alladio, Marcello Baricco, Vincenzo Leogrande, Renato Pagliari, Fabio Pozzi, Paolo Foglio, Marco Vincenti
Software Mentions: 15
Published: over 3 years ago

10.3390/cancers12051142

Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer
Cited by: 55
Author(s): Marc Clos-García, Koldo Garcia, Cristina Alonso, Marta Iruarrizaga‐Lejarreta, Mauro D’Amato, Anais Crespo, Águeda Iglesias, Joaquín Cubiella, Luís Bujanda, Juan Manuel Falcón‐Pérez
Software Mentions: 14
Published: over 4 years ago

10.1186/s12859-016-1455-1

MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration
Cited by: 20
Author(s): Carles Hernández-Ferrer, Carlos Ruiz‐Arenas, Alba Beltran-Gomila, Juan R. González
Software Mentions: 14
Published: almost 8 years ago

10.1016/j.immuni.2021.05.010

Longitudinal analysis reveals that delayed bystander CD8+ T cell activation and early immune pathology distinguish severe COVID-19 from mild disease
Cited by: 188
Author(s): Laura Bergamaschi, Federica Mescia, Lorinda Turner, Aimee L. Hanson, Prasanti Kotagiri, Benjamin J. Dunmore, Hélène Ruffieux, Aloka De, Oisín Huhn, Michael D. Morgan, Pehuén Pereyra Gerber, Mark R. Wills, Stephen Baker, Fernando J Calero-Nieto, Rainer Döffinger, Gordon Dougan, Anne Elmer, Ian Goodfellow, Ravindra Gupta, Myra Hosmillo, Kelvin Hunter, Nathalie Kingston, Paul J. Lehner, Nicholas J Matheson, Jeremy K. Nicholson, A. M. Petrunkina, Sylvia Richardson, Caroline Saunders, James Thaventhiran, Erik J. M. Toonen, Michael P. Weekes, Berthold Göttgens, Mark Toshner, Christoph Hess, John R. Bradley, Paul Lyons, Kenneth Smith
Software Mentions: 12
Published: over 3 years ago

10.3390/s21134377

Multivariate Time Series Analysis of Temperatures in the Archaeological Museum of L’Almoina (Valencia, Spain)
Cited by: 4
Author(s): Sandra Ramírez, Manuel Zarzo, Fernando-Juan García-Diego
Software Mentions: 12
Published: over 3 years ago

10.1186/s12859-020-3360-x

ShinyOmics: collaborative exploration of omics-data
Cited by: 11
Author(s): Defne Surujon, Tim van Opijnen
Software Mentions: 11
Published: almost 5 years ago

10.1186/s13059-020-1926-6

Eleven grand challenges in single-cell data science
Cited by: 646
Author(s): David Laehnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie Hicks, Mark D. Robinson, Catalina A. Vallejos, Kieran R Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan‐Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M Keizer, Indu Khatri, Szymon M. Kiełbasa, Jan Korbel, Alexey M Kozlov, Tzu Hao Kuo, Boudewijn P. F. Lelieveldt, Ion Măndoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Łukasz Rączkowski, Marcel J. T. Reinders, Jeroen de Ridder, Antoine Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alexander Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth
Software Mentions: 11
Published: almost 5 years ago

10.7717/peerj.1845

A molecular classification of human mesenchymal stromal cells
Cited by: 42
Author(s): Florian Rohart, Elizabeth A. Mason, Nicholas Matigian, Rowland Mosbergen, Othmar Korn, Tyrone Chen, Suzanne Butcher, Jatin Patel, Kerry Atkinson, Kiarash Khosrotehrani, Nicholas M. Fisk, Kim‐Anh Lê Cao, Christine A. Wells
Software Mentions: 10
Published: over 8 years ago

10.3390/s21020436

A Methodology for Discriminant Time Series Analysis Applied to Microclimate Monitoring of Fresco Paintings
Cited by: 8
Author(s): Sandra Ramírez, Manuel Zarzo, Ángel Perles, Fernando-Juan García-Diego
Software Mentions: 10
Published: almost 4 years ago

10.1371/journal.pone.0251804

Influence of genetic background and dietary oleic acid on gut microbiota composition in Duroc and Iberian pigs
Cited by: 4
Author(s): Adrián López-García, Rita Benítez, Yolanda Núñez, E. Gómez-Izquierdo, E. de Mercado, Juan García‐Casco, Óscar González-Recio, C. J. López‐Bote, Jordi Estellé, Cristina Óvilo
Software Mentions: 10
Published: over 3 years ago

10.34133/2020/8954085

Machine Learning-Based Presymptomatic Detection of Rice Sheath Blight Using Spectral Profiles
Cited by: 23
Author(s): Anna O. Conrad, Wei Li, Da-Young Lee, Guo‐Liang Wang, Luis E. Rodriguez‐Saona, Pierluigi Bonello
Software Mentions: 10
Published: almost 5 years ago

10.1186/s40168-019-0745-z

Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation
Cited by: 57
Author(s): Anna Cäcilia Ingham, Katrine Kielsen, Malene Skovsted Cilieborg, Ole Lund, Susan Holmes, Frank Møller Aarestrup, Klaus Müller, Sünje Johanna Pamp
Software Mentions: 9
Published: over 5 years ago

10.3389/fpls.2019.01355

In-Field Detection and Quantification of Septoria Tritici Blotch in Diverse Wheat Germplasm Using Spectral–Temporal Features
Cited by: 22
Author(s): Jonas Anderegg, Andreas Hund, Petteri Karisto, Alexey Mikaberidze
Software Mentions: 9
Published: about 5 years ago

10.1186/s13062-021-00293-8

Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers
Cited by: 7
Author(s): Sergio Romera-Giner, Zoraida Andreu Martínez, Francisco García‐García, Marta R. Hidalgo
Software Mentions: 9
Published: over 3 years ago

10.3389/fmicb.2020.556793

Sulfate Alters the Competition Among Microbiome Members of Sediments Chronically Exposed to Asphalt
Cited by: 3
Author(s): Antonios Michas, Mourad Harir, Marianna Lucio, Gisle Vestergaard, Anne M. Himmelberg, Philippe Schmitt‐Kopplin, Tillmann Lueders, Dimitris G. Hatzinikolaou, Anne Schöler, Ralf Rabus, Michael Schloter
Software Mentions: 9
Published: about 4 years ago

10.1186/s12866-020-1704-3

The canine oral microbiome: variation in bacterial populations across different niches
Cited by: 36
Author(s): Avika Ruparell, Taichi Inui, Ruth Staunton, Corrin Wallis, Oliver Deusch, Lucy J. Holcombe
Software Mentions: 9
Published: almost 5 years ago

10.3389/fmicb.2020.579427

Environmental and Microbial Interactions Shape Methane-Oxidizing Bacterial Communities in a Stratified Lake
Cited by: 12
Author(s): Carole Guggenheim, Remo Freimann, Magdalena Mayr, Karin Beck, Bernhard Wehrli, Helmut Bürgmann
Software Mentions: 8
Published: about 4 years ago

10.1177/1177932219899051

Multi-omics Data Integration, Interpretation, and Its Application
Cited by: 527
Author(s): Indhupriya Subramanian, Srikant Verma, Sanjiv Kumar, Abhay Jere, Krishanpal Anamika
Software Mentions: 8
Published: almost 5 years ago

10.1128/mSystems.00852-20

Virulence of the Pathogen Porphyromonas gingivalis Is Controlled by the CRISPR-Cas Protein Cas3
Cited by: 16
Author(s): José O. Solbiati, Ana E. Duran-Pinedo, Fernanda Godoy Rocha, Frank C. Gibson, Jorge Frias-Lopez
Software Mentions: 8
Published: about 4 years ago

10.1038/s41598-020-62354-8

Differential stromal reprogramming in benign and malignant naturally occurring canine mammary tumours identifies disease-modulating stromal components
Cited by: 18
Author(s): Parisa Amini, Sina Nassiri, Alexandra Malbon, Enni Markkanen
Software Mentions: 8
Published: over 4 years ago

10.1155/2021/8892849

Correlation Analysis between GDM and Gut Microbial Composition in Late Pregnancy
Cited by: 17
Author(s): Genxia Li, Pan Yin, Shuhui Chu, Wen Gao, Shihong Cui, Shuhua Guo, Yajuan Xu, Enwu Yuan, Texuan Zhu, Jie You, Junya Zhang, Manman Yang
Software Mentions: 8
Published: almost 4 years ago

10.1111/1462-2920.15314

Metagenomic assessment of the global diversity and distribution of bacteria and fungi
Cited by: 39
Author(s): Mohammad Bahram, Tarquin Netherway, Clémence Frioux, Pamela Ferretti, Luís Pedro Coelho, Stefan Geisen, Peer Bork, Falk Hildebrand
Software Mentions: 7
Published: about 4 years ago

10.1002/ece3.7901

Linking ecology, morphology, and metabolism: Niche differentiation in sympatric populations of closely related species of the genus <i>Littorina</i> (<i>Neritrema</i>)
Cited by: 7
Author(s): Arina L. Maltseva, Marina A. Varfolomeeva, Roman V. Ayanka, Elizaveta R. Gafarova, Egor A. Repkin, Polina Pavlova, Alexei L. Shavarda, Natalia A. Mikhailova, Andrei I. Granovitch
Software Mentions: 7
Published: over 3 years ago

10.1128/mBio.03601-20

Ketogenic Diets Induced Glucose Intolerance and Lipid Accumulation in Mice with Alterations in Gut Microbiota and Metabolites
Cited by: 15
Author(s): Yue Li, Yifan Yang, Jing Zhang, Tianyi Jiang, Ziyi Zhang, Zhiyi Wang, Mengxue Gong, Liping Zhao, Chenhong Zhang
Software Mentions: 7
Published: over 3 years ago

10.3390/microorganisms9091939

Human Milk Oligosaccharide-Stimulated Bifidobacterium Species Contribute to Prevent Later Respiratory Tract Infections
Cited by: 18
Author(s): Shaillay Kumar Dogra, François-Pierre Martin, Dominique Donnicola, Monique Julita, Bernard Berger, Norbert Sprenger
Software Mentions: 7
Published: over 3 years ago

10.3390/biomedicines9050454

mRNA Profiles of Porcine Parathyroid Glands Following Variable Phosphorus Supplies throughout Fetal and Postnatal Life
Cited by: 8
Author(s): Michael Oster, Henry Reyer, Christian Gerlinger, Nares Trakooljul, Puntita Siengdee, Jonas Keiler, Siriluck Ponsuksili, Petra Wolf, Klaus Wimmers
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-019-46118-7

Unraveling the effects of the gut microbiota composition and function on horse endurance physiology
Cited by: 24
Author(s): Sandra Plancade, Allison Clark, Catherine Philippe, Jean‐Christophe Helbling, Marie‐Pierre Moisan, Diane Esquerré, Laurence Le Moyec, Céline Robert, Éric Barrey, Núria Mach
Software Mentions: 7
Published: over 5 years ago

10.1128/mBio.01432-18

A Natural History of Actinic Keratosis and Cutaneous Squamous Cell Carcinoma Microbiomes
Cited by: 31
Author(s): David Wood, Nancy Lachner, Jean-Marie Tan, Stephanie Tang, Nicola Angel, Antonia Laino, Richard Linedale, Kim‐Anh Lê Cao, Mark Morrison, Ian H. Frazer, H. Peter Soyer, Philip Hugenholtz
Software Mentions: 7
Published: about 6 years ago

10.3389/fmolb.2021.656204

Understanding the Holobiont: Crosstalk Between Gut Microbiota and Mitochondria During Long Exercise in Horse
Cited by: 12
Author(s): Núria Mach, Marco Moroldo, Andrea Rau, Jérôme Lecardonnel, Laurence Le Moyec, Céline Robert, Éric Barrey
Software Mentions: 7
Published: over 3 years ago

10.1128/mBio.03701-20

Inter- and Intra-Annual Bacterioplankton Community Patterns in a Deepwater Sub-Arctic Region: Persistent High Background Abundance of Putative Oil Degraders
Cited by: 8
Author(s): Angelina Angelova, Barbara Berx, Eileen Bresnan, Samantha B. Joye, Andrew Free, Tony Gutiérrez
Software Mentions: 7
Published: over 3 years ago

10.1186/s12967-019-2073-2

Bringing radiomics into a multi-omics framework for a comprehensive genotype–phenotype characterization of oncological diseases
Cited by: 63
Author(s): Mario Zanfardino, Monica Franzese, Katia Pane, Carlo Cavaliere, Serena Monti, Giuseppina Esposito, Marco Salvatore, Marco Aiello
Software Mentions: 6
Published: about 5 years ago

10.1186/s13059-015-0741-y

Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data
Cited by: 222
Author(s): Jean Philippe Fortin, Kasper D. Hansen
Software Mentions: 6
Published: over 9 years ago

10.1002/ece3.2206

Are the metabolomic responses to folivory of closely related plant species linked to macroevolutionary and plant-folivore coevolutionary processes?
Cited by: 14
Author(s): Albert Rivas‐Ubach, José A. Hódar, Jordi Sardans, Jennifer Kyle, Young Mo Kim, Michal Oravec, Otmar Urban, Alex Guenther, Josep Peñuelas
Software Mentions: 6
Published: over 8 years ago

10.1186/s12859-019-3224-4

Vertical and horizontal integration of multi-omics data with miodin
Cited by: 35
Author(s): Benjamin Ulfenborg
Software Mentions: 6
Published: about 5 years ago

10.3389/fvets.2019.00214

Transcriptomic Profiling of Duodenal Epithelium Reveals Temporally Dynamic Impacts of Direct Duodenal Starch-Infusion During Dry Period of Dairy Cattle
Cited by: 2
Author(s): Congjun Li, Shudai Lin, María Jose Ranilla-García, VI Ransom L. Baldwin
Software Mentions: 6
Published: over 5 years ago

10.3389/fpls.2018.00857

Metabolite Profiles of Sugarcane Culm Reveal the Relationship Among Metabolism and Axillary Bud Outgrowth in Genetically Related Sugarcane Commercial Cultivars
Cited by: 21
Author(s): Danilo Alves Ferreira, Marina C. M. Martins, Adriana Cheavegatti-Gianotto, Monalisa Sampaio Carneiro, Rodrigo R. Amadeu, Juliana Aparecida Aricetti, L. D. Wolf, Hermann Paulo Hoffmann, Luís Guilherme F. de Abreu, Camila Caldana
Software Mentions: 6
Published: over 6 years ago

10.3390/metabo11040236

Metabolite Profile of Treatment-Naive Metabolic Syndrome Subjects in Relation to Cardiovascular Disease Risk
Cited by: 5
Author(s): Moritz V. Warmbrunn, Annefleur M. Koopen, Nicolien C. de Clercq, Pieter F. de Groot, Ruud S. Kootte, Kristien E. Bouter, Kasper W. ter Horst, Annick V. Hartstra, Mireille J. Serlie, Mariëtte T. Ackermans, Maarten R. Soeters, Daniël H. van Raalte, Mark Davids, Max Nieuwdorp, Albert K. Groen
Software Mentions: 6
Published: over 3 years ago

10.7554/eLife.50069

Metabolic stress is a primary pathogenic event in transgenic Caenorhabditis elegans expressing pan-neuronal human amyloid beta
Cited by: 49
Author(s): Emelyne Teo, Sudharshan Ravi, Diogo Barardo, Hyung-Seok Kim, Sheng Fong, Amaury Cazenave-Gassiot, Tsze Yin Tan, Jianhong Ching, Jean‐Paul Kovalik, Markus R. Wenk, Rudiyanto Gunawan, Philip K. Moore, Barry Halliwell, Nicholas S. Tolwinski, Jan Gruber
Software Mentions: 6
Published: about 5 years ago

10.3390/pathogens8040195

An Acute Stress Model in New Zealand White Rabbits Exhibits Altered Immune Response to Infection with West Nile Virus
Cited by: 5
Author(s): Willy W. Suen, Mitchell Imoda, Albert W Thomas, Nur N B M Nasir, Nawaporn Tearnsing, Wenqi Wang, Helle Bielefeldt‐Ohmann
Software Mentions: 6
Published: about 5 years ago

10.7554/eLife.65776

Developing a multivariate prediction model of antibody features associated with protection of malaria-infected pregnant women from placental malaria
Cited by: 18
Author(s): Elizabeth H. Aitken, Timon Damelang, Amaya Ortega-Pajares, Agersew Alemu, Wina Hasang, Saber Dini, Holger W. Unger, Maria Ome-Kaius, Morten A. Nielsen, Ali Salanti, Joe Smith, Stephen J. Kent, P Mark Hogarth, Bruce D. Wines, Julie A. Simpson, Amy W. Chung, Stephen J. Rogerson
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-94256-8

Proteomics and metabonomics analyses of Covid-19 complications in patients with pulmonary fibrosis
Cited by: 10
Author(s): Jianrong Yang, Chunxia Chen, Wan Chen, Luying Huang, Zhao Fu, Kun Ye, Liwen Lv, Zhihuang Nong, Xing Zhou, Wensheng Lu, Ming Zhong
Software Mentions: 6
Published: over 3 years ago

10.3390/microorganisms8081225

Lactobacillus Mucosae Strain Promoted by a High-Fiber Diet in Genetic Obese Child Alleviates Lipid Metabolism and Modifies Gut Microbiota in ApoE-/- Mice on a Western Diet
Cited by: 19
Author(s): Tianyi Jiang, Huan Wu, Xin Yang, Yue Li, Ziyi Zhang, Feng Chen, Liping Zhao, Chenhong Zhang
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-021-87886-5

Metabolomics and transcriptomics to decipher molecular mechanisms underlying ectomycorrhizal root colonization of an oak tree
Cited by: 14
Author(s): Mónica Sebastiana, Albert Gargallo‐Garriga, Jordi Sardans, Míriam Pérez‐Trujillo, Filipa Monteiro, Andreia Figueiredo, Marisa Maia, Rui Nascimento, Marta Sousa Silva, António E. N. Ferreira, Carlos Cordeiro, A. Marques, Lisete Sousa, Rui Malhó, Josep Peñuelas
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-82306-0

Terroir and vintage discrimination of Malbec wines based on phenolic composition across multiple sites in Mendoza, Argentina
Cited by: 17
Author(s): Roy Urvieta, Gregory V. Jones, Fernando Buscema, Rubén Bottini, A. Fontana
Software Mentions: 6
Published: almost 4 years ago

10.3390/metabo4020433

Influence of Missing Values Substitutes on Multivariate Analysis of Metabolomics Data
Cited by: 139
Author(s): Piotr S. Gromski, Yun Xu, Helen L. Kotze, Elon Correa, David I. Ellis, Emily G. Armitage, Michael L. Turner, Royston Goodacre
Software Mentions: 6
Published: over 10 years ago

10.3390/microorganisms8111741

Bile Acid Signal Molecules Associate Temporally with Respiratory Inflammation and Microbiome Signatures in Clinically Stable Cystic Fibrosis Patients
Cited by: 11
Author(s): Stephanie Flynn, F. Jerry Reen, José A. Caparrós-Martín, David F. Woods, Jörg Peplies, Sarath Ranganathan, Stephen M. Stick, Fergal O’Gara
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-021-93468-2

Integrative biology defines novel biomarkers of resistance to strongylid infection in horses
Cited by: 5
Author(s): Guillaume Sallé, Cécile Canlet, Jacques Cortet, Christine Koch, Joshua Malsa, Fabrice Reigner, Mickaël Riou, Noémie Perrot, Alexandra Blanchard, Núria Mach
Software Mentions: 6
Published: over 3 years ago

10.3389/fnins.2021.591122

Single-Cell Transcriptomics: Current Methods and Challenges in Data Acquisition and Analysis
Cited by: 40
Author(s): Asif Adil, Vijay Kumar, Arif Tasleem Jan, M. Asger
Software Mentions: 6
Published: over 3 years ago

10.3389/fcell.2020.582320

Microbiome Profiling Reveals Gut Dysbiosis in the Metabotropic Glutamate Receptor 5 Knockout Mouse Model of Schizophrenia
Cited by: 15
Author(s): Carolina Gubert, Geraldine Kong, Volkan Uzungil, Ariel M Zeleznikow-Johnston, Emma L. Burrows, Thibault Renoir, Anthony J Hannan
Software Mentions: 6
Published: about 4 years ago

10.1007/s11306-016-1030-9

Non-targeted UHPLC-MS metabolomic data processing methods: a comparative investigation of normalisation, missing value imputation, transformation and scaling
Cited by: 211
Author(s): Riccardo Di Guida, Jasper Engel, J. William Allwood, Ralf J. M. Weber, Steven J.M. Jones, Ulf Sommer, Mark R. Viant, Warwick B. Dunn
Software Mentions: 6
Published: over 8 years ago

10.1186/s40104-021-00584-0

Weaning-associated feed deprivation stress causes microbiota disruptions in a novel mucin-containing in vitro model of the piglet colon (MPigut-IVM)
Cited by: 6
Author(s): Raphaële Gresse, Frédérique Chaucheyras‐Durand, Sylvain Denis, Martín Beaumont, Tom Van de Wiele, Evelyne Forano, Stéphanie Blanquet-Diot
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2017.02222

Gut Microbial Dysbiosis Is Associated with Altered Hepatic Functions and Serum Metabolites in Chronic Hepatitis B Patients
Cited by: 126
Author(s): Jing Wang, Yang Wang, Xu Zhang, Jiaqi Liu, Qianpeng Zhang, Yu Zhao, Jinghua Peng, Qin Feng, Jianye Dai, Shujun Sun, Yuwu Zhao, Liping Zhao, Yongyu Zhang, Yiyang Hu, Menghui Zhang
Software Mentions: 6
Published: about 7 years ago

10.1038/s41598-020-62911-1

Analyzing the impact of Mycobacterium tuberculosis infection on primary human macrophages by combined exploratory and targeted metabolomics
Cited by: 25
Author(s): Frank Vrieling, Sarantos Kostidis, Herman P. Spaink, Mariëlle C. Haks, Oleg A. Mayboroda, Tom H. M. Ottenhoff, Simone A. Joosten
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0128854

ONION: Functional Approach for Integration of Lipidomics and Transcriptomics Data
Cited by: 5
Author(s): Monika Piwowar, Wiktor Jurkowski
Software Mentions: 6
Published: over 9 years ago

10.3390/jpm10040271

Identification of Metabolic Biomarkers in Relation to Methotrexate Response in Early Rheumatoid Arthritis
Cited by: 13
Author(s): Helen R. Gosselt, Ittai B. Muller, Gerrit Jansen, Michel van Weeghel, Frédéric M. Vaz, Johanna M. W. Hazes, Sandra G. Heil, Robert de Jonge
Software Mentions: 5
Published: about 4 years ago

10.1186/s12866-016-0885-2

The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass, Dicentrarchus labrax, submitted to different nutritional histories
Cited by: 41
Author(s): François-Joël Gatesoupe, Christine Huelvan, Nicolas Le Bayon, Hervé Le Delliou, Lauriane Madec, Olivier Mouchel, Patrick Quazuguel, David Mazurais, José‐Luis Zambonino-Infante
Software Mentions: 5
Published: about 8 years ago

10.1016/j.isci.2021.103048

Post-weaning A1/A2 β-casein milk intake modulates depressive-like behavior, brain μ-opioid receptors, and the metabolome of rats
Cited by: 5
Author(s): Aya Osman, Simone Zuffa, Gemma Walton, Elizabeth Fagbodun, Panos Zanos, Polymnia Georgiou, Ian Kitchen, Jonathan R. Swann, Alexis Bailey
Software Mentions: 5
Published: over 3 years ago

10.1002/cti2.1093

Machine learning applied to whole‐blood RNA‐sequencing data uncovers distinct subsets of patients with systemic lupus erythematosus
Cited by: 39
Author(s): William A. Figgett, Katherine Monaghan, Milica Ng, Monther Alhamdoosh, Eugene Maraskovsky, Nicholas J. Wilson, Alberta Hoi, Eric F Morand, Fabienne Mackay
Software Mentions: 5
Published: almost 6 years ago

10.1016/j.csbj.2019.04.009

Accounting for biological variation with linear mixed-effects modelling improves the quality of clinical metabolomics data
Cited by: 26
Author(s): Kwanjeera Wanichthanarak, Saharuetai Jeamsripong, Natapol Pornputtapong, Sakda Khoomrung
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41438-021-00465-7

Genetic characterization of an almond germplasm collection and volatilome profiling of raw and roasted kernels
Cited by: 10
Author(s): Mario Di Guardo, Brian Farneti, Iuliia Khomenko, Giulia Modica, A. Mosca, Gaetano Distefano, Luca Bianco, Michela Troggio, Francesco Sottile, Stefano La Malfa, Franco Biasioli, Alessandra Gentile
Software Mentions: 5
Published: almost 4 years ago

10.1186/s40246-020-00291-3

Aldh1l2 knockout mouse metabolomics links the loss of the mitochondrial folate enzyme to deregulation of a lipid metabolism observed in rare human disorder
Cited by: 9
Author(s): Natalia I. Krupenko, Jaspreet Sharma, Peter Pediaditakis, Kristi L. Helke, Madeline S. Hall, Xiuxia Du, Susan Sumner, Sergey A. Krupenko
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0067907

Gene-Metabolite Expression in Blood Can Discriminate Allergen-Induced Isolated Early from Dual Asthmatic Responses
Cited by: 18
Author(s): Amrit Singh, Masatsugu Yamamoto, Sarah Kam, Jian Ruan, Gail M. Gauvreau, Paul M. O'Byrne, J. Mark FitzGerald, R. Robert Schellenberg, Louis‐Philippe Boulet, Gabriella Wojewodka, Cynthia Kanagaratham, Juan B. De Sanctis, Danuta Radzioch, Scott J. Tebbutt
Software Mentions: 5
Published: over 11 years ago

10.1016/j.ebiom.2019.06.041

Metabolomics in plasma of Malawian children 7 years after surviving severe acute malnutrition: “ChroSAM” a cohort study
Cited by: 14
Author(s): Céline Bourdon, Natasha Lelijveld, Debbie Thompson, Prasad S. Dalvi, Gerard Bryan Gonzales, Dominic Wang, Misagh Alipour, Eytan Wine, Emmanuel Chimwezi, Jonathan C. K. Wells, Marko Kerac, Robert Bandsma, Moffat Nyirenda
Software Mentions: 5
Published: over 5 years ago

10.3389/fpls.2020.01140

Development of a Novel Phenotypic Roadmap to Improve Blueberry Quality and Storability
Cited by: 10
Author(s): Brian Farneti, F. Emanuelli, Iuliia Khomenko, M. Ajelli, Franco Biasioli, L. Giongo
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2021.703421

Pathogen Challenge and Dietary Shift Alter Microbiota Composition and Activity in a Mucin-Associated in vitro Model of the Piglet Colon (MPigut-IVM) Simulating Weaning Transition
Cited by: 5
Author(s): Raphaële Gresse, Frédérique Chaucheyras‐Durand, Juan J. Garrido, Sylvain Denis, Ángeles Jiménez-Marín, Martín Beaumont, Tom Van de Wiele, Evelyne Forano, Stéphanie Blanquet‐Diot
Software Mentions: 5
Published: over 3 years ago

10.3390/cancers12113199

Regulation of Canonical Oncogenic Signaling Pathways in Cancer via DNA Methylation
Cited by: 13
Author(s): Jennifer Lu, Premila M Wilfred, Darren Korbie, Matt Trau
Software Mentions: 5
Published: about 4 years ago

10.3390/biom9100586

Allogenic Faecal Microbiota Transfer Induces Immune-Related Gene Sets in the Colon Mucosa of Patients with Irritable Bowel Syndrome
Cited by: 5
Author(s): Savanne Holster, Guido Hooiveld, Dirk Repsilber, Willem M. de Vos, Robert Jan Brummer, Julia König
Software Mentions: 5
Published: about 5 years ago

10.1186/s12859-019-3291-6

DeepMF: deciphering the latent patterns in omics profiles with a deep learning method
Cited by: 10
Author(s): Lingxi Chen, Jianjun Xu, Shuai Cheng Li
Software Mentions: 5
Published: about 5 years ago

10.3389/fmicb.2017.02293

Resource Legacies of Organic and Conventional Management Differentiate Soil Microbial Carbon Use
Cited by: 35
Author(s): Melissa M. Arcand, David J. Levy‐Booth, Bobbi L. Helgason
Software Mentions: 5
Published: about 7 years ago

10.3389/fmicb.2015.00024

Resuscitation of the rare biosphere contributes to pulses of ecosystem activity
Cited by: 150
Author(s): Zachary T. Aanderud, Stuart Jones, Noah Fierer, Jay T. Lennon
Software Mentions: 5
Published: almost 10 years ago

10.3390/microorganisms8071073

Maturational Changes Alter Effects of Dietary Phytase Supplementation on the Fecal Microbiome in Fattening Pigs
Cited by: 7
Author(s): Barbara U. Metzler‐Zebeli, Jutamat Klinsoda, Julia Vötterl, Doris Verhovsek
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-021-84925-z

Ants modulate stridulatory signals depending on the behavioural context
Cited by: 6
Author(s): Alberto Masoni, Filippo Frizzi, Rachele Nieri, Luca Pietro Casacci, Valerio Mazzoni, Stefano Turillazzi, Giacomo Santini
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-020-77846-w

Differential proteomic analysis by SWATH-MS unravels the most dominant mechanisms underlying yeast adaptation to non-optimal temperatures under anaerobic conditions
Cited by: 20
Author(s): Tânia Pinheiro, Ka Ying Florence Lip, Estéfani García‐Ríos, Amparo Querol, J. A. Teixeira, Walter van Gulik, José Manuel Guillamón, Lucı́lia Domingues
Software Mentions: 5
Published: about 4 years ago

10.3389/fmicb.2018.02784

The Influence of Viable Cells and Cell-Free Extracts of Lactobacillus casei on Volatile Compounds and Polyphenolic Profile of Elderberry Juice
Cited by: 17
Author(s): Annalisa Ricci, Alessia Levante, Martina Cirlini, Luca Calani, Valentina Bernini, Daniele Del Rio, Gianni Galaverna, Erasmo Neviani, Camilla Lazzi
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0160169

MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities
Cited by: 125
Author(s): Kim‐Anh Lê Cao, Mary-Ellen Costello, Vanessa Lakis, François Bartolo, Xin-Yi Chua, Rémi Brazeilles, Pascale Rondeau
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-019-41452-2

Using Bacterial Transcriptomics to Investigate Targets of Host-Bacterial Interactions in Caenorhabditis elegans
Cited by: 21
Author(s): Jason P. Chan, Justin Wright, Hoi Tong Wong, Anastasia Ardasheva, Jamey T. Brumbaugh, Christopher J. McLimans, Regina Lamendella
Software Mentions: 5
Published: over 5 years ago

10.1186/1756-0381-5-19

Visualising associations between paired ‘omics’ data sets
Cited by: 211
Author(s): Ignacio González, Kim‐Anh Lê Cao, Melissa J. Davis, Sébastien Déjean
Software Mentions: 5
Published: about 12 years ago

10.1371/journal.ppat.1009097

Vaginal microbiome-hormonal contraceptive interactions associate with the mucosal proteome and HIV acquisition
Cited by: 17
Author(s): Laura Noël‐Romas, Michelle Perner, Refilwe P. Molatlhegi, Christina Farr Zuend, Amanda Mabhula, Sarah Hoger, Alana Lamont, Kenzie Birse, Alicia R. Berard, Stuart McCorrister, Garett Westmacott, Al Leslie, Vanessa Poliquin, Renee Heffron, Lyle R. McKinnon, Adam Burgener
Software Mentions: 5
Published: almost 4 years ago

10.1186/s40168-018-0417-4

Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota
Cited by: 56
Author(s): Jane A. Mullaney, J. Stephens, Mary Ellen Costello, Cai Fong, Brooke E. Geeling, Patrick G. Gavin, Casey M. Wright, Timothy D. Spector, Matthew A. Brown, Emma E. Hamilton‐Williams
Software Mentions: 5
Published: almost 7 years ago

10.3389/fimmu.2020.584116

Rheumatoid Arthritis Synovial Fluid Neutrophils Drive Inflammation Through Production of Chemokines, Reactive Oxygen Species, and Neutrophil Extracellular Traps
Cited by: 62
Author(s): Helen L. Wright, Max Lyon, Elinor A Chapman, Robert J. Moots, Steven W. Edwards
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.ppat.1009101

RV144 HIV-1 vaccination impacts post-infection antibody responses
Cited by: 12
Author(s): Thembi Mdluli, Ningbo Jian, Bonnie M. Slike, Dominic Paquin‐Proulx, G. Donofrio, Aljawharah Alrubayyi, Syna Kuriakose Gift, Rebecca Grande, Mary Bryson, Anna Lee, Vincent Dussupt, Letzibeth Mendez-Riveria, Eric Sanders‐Buell, Agnès‐Laurence Chenine, Ursula Tran, Yifan Li, Eric N. Brown, Paul T. Edlefsen, Robert J. O’Connell, Peter B. Gilbert, Sorachai Nitayaphan, Punnee Pitisuttihum, Supachai Rerks-Ngarm, Merlin L. Robb, Robert A. Gramzinski, Galit Alter, Sodsai Tovanabutra, Ivelin S. Georgiev, Margaret E. Ackerman, Victoria R. Polonis, Sandhya Vasan, Nelson L. Michael, Jerome H. Kim, Michael A. Eller, Shelly J. Krebs, Morgane Rolland
Software Mentions: 5
Published: about 4 years ago

10.3389/fcimb.2020.588155

Proteome and Microbiome Mapping of Human Gingival Tissue in Health and Disease
Cited by: 14
Author(s): Kai Bao, Xiaofei Li, Lucy Poveda, Weihong Qi, Nathalie Selevsek, Pınar Gümüş, Gülnur Emingil, Jonas Grossmann, Patricia I. Diaz, George Hajishengallis, Nagihan Bostancı, Georgios N. Belibasakis
Software Mentions: 5
Published: about 4 years ago

10.3945/ajcn.116.130518

Mortality in children with complicated severe acute malnutrition is related to intestinal and systemic inflammation: an observational cohort study
Cited by: 102
Author(s): Suzanna Attia, Christian J. Versloot, Wieger Voskuijl, Sara J. van Vliet, Valeria Di Giovanni, Ling Zhang, Susan E. Richardson, Céline Bourdon, Mihai G. Netea, James A. Berkley, Patrick F. van Rheenen, Robert Bandsma
Software Mentions: 5
Published: about 8 years ago

10.3389/fcell.2021.667852

Metabolic and Immunological Subtypes of Esophageal Cancer Reveal Potential Therapeutic Opportunities
Cited by: 8
Author(s): Ryan J. King, Fang Qiu, Fang Yu, Pankaj K. Singh
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2105-13-326

A computational pipeline for the development of multi-marker bio-signature panels and ensemble classifiers
Cited by: 29
Author(s): Oliver P. Günther, Virginia Chen, Gabriela Cohen Freue, Robert Balshaw, Scott J. Tebbutt, Zsuzsanna Hollander, Mandeep Takhar, W. Robert McMaster, Bruce M. McManus, Paul Keown, Raymond T. Ng
Software Mentions: 5
Published: about 12 years ago

10.1007/s11306-015-0927-z

GC–MS metabolic profiling of Cabernet Sauvignon and Merlot cultivars during grapevine berry development and network analysis reveals a stage- and cultivar-dependent connectivity of primary metabolites
Cited by: 51
Author(s): Álvaro Cuadros-Inostroza, Simón Ruíz-Lara, Enrique González, Änne Eckardt, Lothar Willmitzer, Hugo Peña‐Cortés
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pone.0167488

Cell-Based Systems Biology Analysis of Human AS03-Adjuvanted H5N1 Avian Influenza Vaccine Responses: A Phase I Randomized Controlled Trial
Cited by: 46
Author(s): Leigh M. Howard, Kristen L. Hoek, Johannes Goll, Parimal Samir, Allison C. Galassie, Tara M. Allos, Xinnan Niu, Laura E. Gordy, C. Buddy Creech, Nripesh Prasad, Travis L. Jensen, Heather Hill, Shawn Levy, Sebastian Joyce, Andrew J. Link, Kathryn M. Edwards
Software Mentions: 5
Published: almost 8 years ago

10.1186/s12866-018-1221-9

Oil type and temperature dependent biodegradation dynamics - Combining chemical and microbial community data through multivariate analysis
Cited by: 50
Author(s): Deni Ribičić, Kelly M. McFarlin, Roman Netzer, Odd Gunnar Brakstad, Anderson M. Winkler, Mimmi Throne-Holst, Trond Røvik Størseth
Software Mentions: 5
Published: over 6 years ago

10.3390/metabo10060220

Non-Targeted Metabolite Profiles and Sensory Properties Elucidate Commonalities and Differences of Wines Made with the Same Variety but Different Cultivar Clones
Cited by: 6
Author(s): Álvaro Cuadros-Inostroza, Claudio Verdugo-Alegría, Lothar Willmitzer, Yerko Moreno-Simunovic, José G. Vallarino
Software Mentions: 4
Published: over 4 years ago

10.1186/s12866-021-02182-6

Potential of fecal microbiota for detection and postoperative surveillance of colorectal cancer
Cited by: 9
Author(s): Qizheng Yao, Meifang Tang, Liuhong Zeng, Zhonghua Chu, Hui Sheng, Yuyu Zhang, Yuan Zhou, Hongyun Zhang, Huayan Jiang, Mingzhi Ye
Software Mentions: 4
Published: over 3 years ago

10.3390/metabo10060218

Age-Dependent Metabolic Profiles Unravel the Metabolic Relationships within and between Flax Leaves (Linum usitatissimum)
Cited by: 10
Author(s): Nicole Pontarin, Roland Molinié, David Mathiron, Job Tchoumtchoua, Solène Bassard, David Gagneul, Benjamin Thiombiano, Hervé Demailly, Jean-Xavier Fontaine, Xavier Guillot, Vivien Sarazin, Anthony Quéro, François Mesnard
Software Mentions: 4
Published: over 4 years ago

Projects: bioconductor: mixOmics

Papers Mentioning mixOmics 375